We can only really speculate as to why Sakurai didn't decide to make him playable. We would need to hear from Sakurai himself on why he decided to only have Isaac as an Assist Trophy and not a playable character.

Did they want to make him a cameo for Brawl, then the next game have him playable?

I must know!

most likely because they simply didn't see 2 games as enough for him to join.Sure the same goes for olimar,but the pikmin-series may have been more successfull than the gs-series,or maybe more iconic or maybe sakurai simply liked it more.

Could Isaac have any cool outfits to resemble other Golden Sun characters?

My outfit thoughts are

AlexFelixMatthewSaturos

Does anyone else have any cool alternative outfit ideas for Isaac?

If Isaac is added to the roster could other Golden Sun characters appear as Assist Trophies?

If so the ones I would like to see are

Saturos and Menardi because these two can use some of their attacks that they use in the final fight on Venus Lighthouse for their assist trophy attacks and they are currently the best end boss in the entire Golden Sun series and if there was any other Golden Sun character appearences, I would like to see Saturos and Menardi and I think they'd make a cool assist trophy.

Mia: she was the main female protagonist in the original Golden Sun and she assists Isaac in that game so why not have her assist Isaac in Super Smash Bros as an assist trophy?